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341 fewer sets in 4DN-only Data.
 

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Project
  • 4DN1049
  • External318
  • ENCODE23
    • Lab
    View 26 More295
    Experiment Category
  • Sequencing831
  • Microscopy559
    • Experiment Type
    View 20 More203
    Dataset
  • Hi-C on ENCODE3 cell lines23
  • Hi-C on synch. HeLa cells - Rep123
  • HCT-116 cohesin-Rad21 degron21
  • FISH for DNA SPRITE19
  • Hi-C on lympoblastoid cell lines from 1000G individuals19
  • Hi-C on synch. HeLa cells - Rep219
  • Liquified Chromatin Hi-C on K652 cells19
  • ChIP-seq on activated B cells17
  • Hi-C on sync. SCC1-AID or CTCF-AID tagged Hela17
  • Hi-C on synch. HeLa cells - Rep317
  • SPT on JM8N4 cells for Spot-On analysis15
  • DNA FISH on Chr1 and Chr1714
  • nascent transcript RNA FISH +/- 13h GATA-1 induction12
  • TSA-seq v1 SON in K56210
  • DNA-FISH in F121-9 cells9
  • HiC on sync. chicken cells9
  • TSA-seq v2 SON in K5629
  • ChIP-seq on Hela SMC3 and CTCF8
  • Cohesin ChIP-seq [29094699]8
  • Hi-C on E14Tg2 cell line8
  • RUES cell differentiation to cardiomyocytes8
  • SPT on U2OS cells8
  • TSA-seq v2 SON in HCT1168
  • nascent transcript RNA FISH - flavopiridol treatment8
  • single cell Hi-C on sorted diploid F1 2-1s8
  • Hi-C on HFF cells - protocol variations7
  • Hi-C on Mouse Olfactory System cells7
  • HiC on sync. CAPH-AID chicken cells7
  • HiC on sync. CAPH2-AID chicken cells7
  • TRIP on K562 cells7
  • DNase Hi-C on Patski +/- Ds-TR and Dxz4 region modfications6
  • Dual color smFISH on fruit fly embryo (nuclear cycle 13)6
  • Hi-C on ES-E14 +/- Mll3-Mll46
  • Hi-C on H9 cells during cardiomyocyte differentiation6
  • Histone mod ChIP-seq [29094699]6
  • TSA-seq v1 LaminA/C in K5626
  • low coverage parameterization6
  • nascent transcript RNA FISH +/- 4h GATA-1 induction6
  • nascent transcript RNA FISH - DRB treatment6
  • Hi-C on activated B cells5
  • Hi-C on mESC during neural differentiation5
  • HiC on sync. chicken cells (no 1NM-PP1 washout)5
  • SMSN (Barentine et al 2019 bioRxiv)5
  • Slc25a37 RNA FISH - enhancer deletion5
  • sci-Hi-C on five human cell lines - analyzed using topic modeling5
  • CTCF ChIP-seq4
  • ChIP-seq in HFFc64
  • ChIP-seq on CH124
  • DNAse Hi-C on RUES cell differentiation to cardiomyocytes4
  • E/L repliseq on EN52.9 mESC with CTCF-AID4
  • E/L repliseq on V6.5 mESC with YY1-dTAG4
  • Hi-C and Micro-C on WTC-11 derived iPS cells4
  • Hi-C on CTCF-AID tagged F123-CASTx1294
  • Hi-C on H1 cells - protocol variations4
  • Hi-C on HAP-1 +/- WAPL or SCC4 KO4
  • Hi-C on WTC-11 differentiation to cardiomyocytes4
  • HiC on sorted sync. SMC2-AID chicken cells4
  • HiC on sorted sync. chicken cells4
  • HiC on unsorted sync. SMC2-AID chicken cells4
  • TCC on IMR90 +/- Adenovirus4
  • TSA-seq v1 LaminB in K5624
  • TSA-seq v1 RBP1 in K5624
  • TSA-seq v1 SON in HCT1164
  • TSA-seq v1 pSC35 in K5624
  • TSA-seq v2 SON in HFFc64
  • nascent transcript RNA FISH - triptolide treatment4
  • ChromEMT3
  • H2A.Z - H13
  • H3K27ac ChIP-seq3
  • Hi-C on CTCF-AID tagged mESCs3
  • Hi-C on HUVEC cell3
  • Hi-C on IMR-903
  • Hi-C on lamin A/C haploinsufficient hiPSC-derived cardiomyocytes3
  • Micro-C on JM8.N4 Cells +/- transcription3
  • RNA-seq [29094699]3
  • RNA-seq on lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes3
  • TCC on hepatocytes +/- NIPBL3
  • single cell Hi-C on sorted haploid H129-1s3
  • ChIA-PET in GM128782
  • ChIA-PET in H1-hESC2
  • ChIA-PET in HFFc62
  • ChIA-PET on CH122
  • DNase Hi-C in Hela-S3 cells +/- SF3B1 siRNA2
  • DNase Hi-C on tissues2
  • DamID-seq on F121-9 cells (2018-10-22)2
  • DamID-seq on H1-hESC cells (2017-12-14)2
  • DamID-seq on HAP-1 cells (2018-10-22)2
  • DamID-seq on HCT116 cells (2018-10-22)2
  • DamID-seq on HFFc6 cells (2017-12-14)2
  • DamID-seq on K562 cells (2018-10-22)2
    • View 90 More599
    Organism
  • Human989
  • Mouse352
  • Chicken40
  • Fruit fly8
  • Green monkey1
    • Sample Type
  • immortalized cells966
  • stem cells285
  • primary cells100
  • induced pluripotent stem cells16
  • tissue9
  • in vitro differentiated cells8
  • whole organisms6
    • Sample Tier
  • Unclassified1116
  • Tier 2162
  • Tier 1112
    • Sample Category
    View 3 More30
    Sample
  • GM1287831
  • H1-hESC (Tier 1)28
  • Patski28
  • GM12878 (Tier 1)27
  • HeLa cell line25
  • F121-9-CASTx129 (Tier 2)24
  • B cell derived cell line22
  • ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion22
  • hepatocyte20
  • DT40 with random integration of X. laevis Cdk1, CDK1 disruption18
  • JM8.N4 (Tier 2)18
  • HCT116 (Tier 2)16
  • H1-hESC (Tier 1) differentiated to definitive endoderm13
  • ES-E14TG2a11
  • CH1210
  • animal zygote9
  • DT40 with random integration of GFP and AID-tagged SMC2 gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of SMC2 gene, SMC2 gene deletion8
  • F123-CASTx129 (Tier 2)8
  • mouse embryonic fibroblast cell8
  • DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion7
  • DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption7
  • F121-6-CASTx1297
  • IMR-907
  • Fruit fly (Oregon-R) embryo - NC135
  • H1-hESC5
  • IMR-90 (Tier 1)5
  • U2OS (Tier 2)5
  • mESC line with Oct4-GFP5
  • olfactory receptor cell5
  • C57BL6-MEF-c54
  • H129-14
  • LMNA-R225X-het with LMNA-R225X corrected to wild-type by Crispr differentiated to cardiac muscle cell4
  • RPE-hTERT (Tier 2)4
  • V6.5 with YY1-dTAG4
  • animal zygote with Wapl deletion4
  • ES-E143
  • ES-E14 with Flo/Flox deletion of Mll3 and Mll4 genes3
  • HAP-1 (Tier 2)3
  • HUVEC cell3
  • RUES23
  • RUES2 differentiated to cardiac muscle cell3
  • RUES2 differentiated to mesoderm3
  • RUES2 differentiated to primitive cardiac myocyte3
  • WTC-11 (Tier 1)3
  • 1926272
  • 46C with Sox1-GFP2
  • C57BL6-MEF2
  • CC-25512
  • CH12.LX2
  • Cas129-CD1-129xCAST2
  • H9 (Tier 2)2
  • HEK293 (Tier 2)2
  • LMNA-R225X-het differentiated to cardiac muscle cell2
  • S22
  • SAEC2
  • SK-N-DZ2
  • V6.52
  • WTC-11 AAVS1-GFP C282
  • WTC-11 AAVS1-GFP C62
  • animal zygote with Rad21 deletion2
  • extraembryonic cell2
  • heart2
  • primary somatosensory cortex (Hes5-GFP/Dcx-mRFP)2
  • A5491
  • ACHN1
  • COS-71
  • Caki21
  • DLD11
  • F121-9-CASTx1291
  • Fruit fly embryo hunchback +/- (NC13)1
  • G1E-ER4 with random integration of ER-responsive GATA-1, GATA-1 gene deletion, Crispr deletion of Slc25a37 enhancer E11
  • G1E-ER4 with random integration of ER-responsive GATA-1, GATA-1 gene deletion, Crispr deletion of Slc25a37 enhancer E21
  • G1E-ER4 with random integration of ER-responsive GATA-1, GATA-1 gene deletion, Crispr deletion of Slc25a37 enhancer E31
  • G1E-ER4 with random integration of ER-responsive GATA-1, GATA-1 gene deletion, Crispr deletion of Slc25a37 enhancers E1-31
  • G4011
  • GM184861
  • GM185051
  • GM185071
  • GM185081
  • GM185161
  • GM185221
  • GM190991
  • GM191411
  • GM191931
  • GM192041
  • GM192381
  • GM192391
  • GM192401
  • H9 with targeted integration of GFP-tagged MYL21
  • H9 with targeted integration of GFP-tagged MYL2 differentiated to cardiac muscle cell1
    • View 90 More520
    Tissue Source
    View 32 More149
    Publication
  • Finn EH et al. (2019) Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.246
  • Abramo K et al. (2019) A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.194
  • No value166
  • Bartman CR et al. (2018) Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptio76
  • Vian L et al. (2018) The Energetics and Physiological Impact of Cohesin Extrusion.75
  • Hansen AS et al. (2018) Robust model-based analysis of single-particle tracking experiments with Spot-On.60
  • Gibcus JH et al. (2018) A pathway for mitotic chromosome formation.42
  • Rao SSP et al. (2017) Cohesin Loss Eliminates All Loop Domains.36
  • Sanborn AL et al. (2015) Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered g35
  • Rao SS et al. (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.34
  • Rivera-Mulia JC et al. (2018) Allele-specific control of replication timing and genome organization during development.33
  • Bonora G et al. (2018) Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.28
  • Chen Y et al. (2018) Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological rule28
  • Liguo Zhang et al. (2019) TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles27
  • Wutz G et al. (2017) Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, W25
  • Quinodoz SA et al. (2018) Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.22
  • Nora EP et al. (2017) Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartme21
  • Schwarzer W et al. (2017) Two independent modes of chromatin organization revealed by cohesin removal.20
  • Gorkin DU et al. (2019) Common DNA sequence variation influences 3-dimensional conformation of the human genome.19
  • Houda Belaghzal et al. (2019) Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C19
  • Bertero A et al. (2019) Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing fact18
  • Bonev B et al. (2017) Multiscale 3D Genome Rewiring during Mouse Neural Development.18
  • Gassler J et al. (2017) A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.15
  • Nagano T et al. (2017) Cell-cycle dynamics of chromosomal organization at single-cell resolution.13
  • Aizhan Bizhanova et al. (2019) Distinct features of nucleolus-associated domains in mouse embryonic stem cells12
  • Sima J et al. (2019) Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.9
  • Charles A. Kenworthy et al. (2017) Genomic binding dynamics of PBAF are regulated via select chromatin states8
  • Leemans C et al. (2019) Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs.7
  • Monahan K et al. (2019) LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice.7
  • Bertero A et al. (2019) Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.6
  • Jian Yan et al. (2017) Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at E6
  • Vertii A et al. (2019) Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin.6
  • Yanxiao Zhang et al. (2019) 3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Role Of HE6
  • Zoller B et al. (2018) Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.6
  • Andrew E S Barentine et al. (2019) 3D Multicolor Nanoscopy at 10,000 Cells a Day5
  • Hyeon-Jin Kim et al. (2019) Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell5
  • Falk M et al. (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei.4
  • Haarhuis JHI et al. (2017) The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.4
  • Haochen Li et al. (2017) Specific Virus-Host Genome Interactions Revealed by Tethered Chromosome Conformation Capture4
  • Naoki Kubo et al. (2017) Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells4
  • Nils Krietenstein et al. (2019) Ultrastructural details of mammalian chromosome architecture4
  • Ray J et al. (2019) Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.4
  • Ou HD et al. (2017) ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.3
  • Tsung-Han S. Hsieh et al. (2019) Resolving the 3D landscape of transcription-linked mammalian chromatin folding3
  • Juric I et al. (2019) MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments2
  • Kim JS et al. (2019) Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing facto2
  • Deng X et al. (2015) Bipartite structure of the inactive mouse X chromosome.1
  • Jin F et al. (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells.1
  • Selvaraj S et al. (2013) Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.1
    • View 39 More426
    Modifications
  • No value1234
  • Crispr114
  • Stable Transfection67
  • Other1
    • Treatments
  • No value1069
  • Chemical301
  • RNAi14
  • Biological4
  • Other4
  • Heat Shock2
    • Assay Details
  • Enzyme: DNaseI21
  • Target: H3K27ac17
  • Target: 3x SV40 NLS-Halo-tag15
  • Target: Ctcf mouse protein15
  • Target: H3K4me315
  • Target: HistoneH2B-Halo-tag15
  • Target: Sox2 mouse protein with HALO tag15
  • Target: H3K27me312
  • Target: RNA Pol II12
  • Target: GRCm38:7:103826534-103827928 mouse region11
  • Target: H2A.Z protein9
  • Target: Rad21 mouse protein9
  • Fraction: late of 2 fractions8
  • Target: H3K4me18
  • Enzyme: MNase7
  • Target: GRCm38:14:69241851-69285103 mouse region7
  • Target: GRCm38:8:84969622-84974811 mouse region7
  • Enzyme: NcoI6
  • Target: CTCF protein, TUBA4A protein, Chromosomes6
  • Target: LMNB1 protein6
  • Target: H3K4me25
  • Target: IgG protein5
  • Target: LaminA/C protein, TUBA4A protein, Chromosomes5
  • Target: NPAT protein5
  • Target: Smc3 mouse protein5
  • Target: TUBA4A protein, CTCF protein, Chromosomes5
  • Target: CTCF protein, TUBA4A protein, Chromosomes, NCAPH protein4
  • Target: Chromosomes, CTCF protein, TUBA4A protein4
  • Target: Chromosomes, RAD21, NCAPH protein, TUBA4A protein4
  • Target: Chromosomes, TUBA4A protein, LaminA/C protein4
  • Target: Chromosomes, TUBA4A protein, RAD214
  • Target: NCAPH protein, TUBA4A protein, Chromosomes, RAD214
  • Target: Nucleolus4
  • Target: Ring2_1b protein4
  • Target: SMC3 protein4
  • Target: SUZ12 protein4
  • Target: TUBA4A protein, Chromosomes, RAD214
  • Target: Chromosomes3
  • Target: Chromosomes, CTCF protein, TUBA4A protein, NCAPH protein3
  • Target: Chromosomes, LaminA/C protein, TUBA4A protein3
  • Target: NCAPH protein, Chromosomes, TUBA4A protein, LaminA/C protein3
  • Target: RAD21, Chromosomes, TUBA4A protein3
  • Target: TUBA4A protein, Chromosomes, LaminA/C protein3
  • Target: TUBA4A protein, Chromosomes, LaminA/C protein, NCAPH protein3
  • Target: TUBA4A protein, RAD21, Chromosomes3
  • Target: TUBA4A protein, RAD21, Chromosomes, NCAPH protein3
  • Enzyme: AluI2
  • Target: CBX5 protein2
  • Target: CTCF protein, TUBA4A protein, Chromosomes, NCAPH protein, LaminA/C protein2
  • Target: Chromosomes, CTCF protein, NCAPH protein, TUBA4A protein2
  • Target: Chromosomes, NCAPH protein, TUBA4A protein, LaminA/C protein2
  • Target: Chromosomes, RAD21, NCAPH protein, TUBA4A protein, LaminA/C protein2
  • Target: GRCh38:17:30541949-30739347 region, Chromosomes, GRCh38:17:69261617-69425619 region, GRCh38:17:33020947-33186327 region2
  • Target: GRCh38:17:36387556-36574537 region, GRCh38:17:30088606-30263568 region, Chromosomes, GRCh38:17:65509811-65678200 region2
  • Target: GRCh38:17:36387556-36574537 region, GRCh38:17:30088606-30263568 region, Chromosomes, GRCh38:17:9734635-9900986 region2
  • Target: GRCh38:17:63767294-63927790 region, GRCh38:17:36387556-36574537 region, GRCh38:17:30088606-30263568 region, Chromosomes2
  • Target: GRCh38:18:2535851-2706101 region, Chromosomes, GRCh38:18:62276743-62456847 region, GRCh38:18:75525179-75695249 region2
  • Target: GRCh38:18:75525179-75695249 region, GRCh38:18:22075002-22239510 region, Chromosomes, GRCh38:18:34992711-35151964 region2
  • Target: GRCm38:11:102348820-102365281 mouse region, GRCm38:7:103826534-103827928 mouse region, GRCm38:4:115056426-115071755 mouse region2
  • Target: GRCm38:11:32283672-32284486 mouse region, GRCm38:8:84969622-84974811 mouse region2
  • Target: GRCm38:14:69241851-69285103 mouse region, GRCm38:8:84969622-84974811 mouse region2
  • Target: GRCm38:15:36595658-36608973 mouse region2
  • Target: GRCm38:15:61985341-61990361 mouse region2
  • Target: GRCm38:4:115056426-115071755 mouse region, GRCm38:10:80409165-80433653 mouse region2
  • Target: GRCm38:6:88193891-88207032 mouse region2
  • Target: GRCm38:7:103826534-103827928 mouse region, GRCm38:8:84969622-84974811 mouse region2
  • Target: GRCm38:7:28808541-28822266 mouse region2
  • Target: GRCm38:8:84901928-84905295 mouse region2
  • Target: GRCm38:8:84969622-84974811 mouse region, GRCm38:14:69241851-69285103 mouse region2
  • Target: GRCm38:8:84969622-84974811 mouse region, GRCm38:15:36595658-36608973 mouse region2
  • Target: H3F3A protein2
  • Target: H3K36me32
  • Target: H3K79me22
  • Target: H3K9me32
  • Target: H4K16Ac2
  • Target: H4K20me32
  • Target: LaminA/C protein2
  • Target: LaminA/C protein, Chromosomes, RAD21, NCAPH protein, TUBA4A protein2
  • Target: LaminB1:B22
  • Target: NCAPH protein, RAD21, TUBA4A protein, Chromosomes2
  • Target: Nipbl mouse protein2
  • Target: PBRM1 protein2
  • Target: PBRM1 protein-6 bromo domains deleted2
  • Target: Polr2a mouse protein2
  • Target: RAD21, TUBA4A protein, Chromosomes2
  • Target: SC35 protein with Phosphorylation2
  • Target: TUBA4A protein, CTCF protein, LaminA/C protein, NCAPH protein, Chromosomes2
  • Target: TUBA4A protein, Chromosomes, NCAPH protein, LaminA/C protein, RAD212
  • Enzyme: MspI1